Re: [galaxy-dev] [galaxy-user] Custom java tool

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: [galaxy-dev] [galaxy-user] Custom java tool

Daniel Blankenberg
Hi Nils,

At this point we're going to go with the approach that jars should be placed in the directory specified by '${GALAXY_DATA_INDEX_DIR}/shared/jars/', ordinarily this is 'GALAXY_ROOT/tool-data/shared/jars/', but the tool-data directory can be configured as the value of the 'tool_data_path' variable in universe_wsgi.ini.


This allows jars to be accessible in tool configurations by specifying e.g. '${GALAXY_DATA_INDEX_DIR}/shared/jars/FOO.jar', where FOO.jar is the desired jar. Let us know if this is inadequate.

(added in changeset: 3844:8fe924966a6a)


Thanks for using Galaxy,

Dan


On May 12, 2010, at 6:03 PM, Nils Homer wrote:

> A jar bin would be great.  That would make it easy to add in new JARs.
>
>
> On 5/12/10 1:22 PM, "Daniel Blankenberg" <[hidden email]> wrote:
>
>> Hi Nils,
>>
>> We do not currently have a best way to directly execute JARs in Galaxy. It
>> does not appear that setting $classpath or $path, etc, will allow the direct
>> execution of jars without providing the path or when not found in the current
>> working directory.
>>
>> One simple possibility is for Galaxy to allow a configurable directory where
>> required JARs can dropped / linked to; this variable would then be available
>> for use in tool configurations.  Do you have any suggestions/ideas/thoughts?
>>
>>
>> Thanks for using Galaxy,
>>
>> Dan
>>
>>
>> On May 6, 2010, at 3:59 AM, Nils Homer wrote:
>>
>>> What is the best way to include wrap a JAR file in galaxy?  Also, what is
>>> the best way to submit tools and their associated wrappers?
>>>
>>> Thank-you for your help in advance,
>>>
>>> Nils Homer
>>>
>>>
>>> _______________________________________________
>>> galaxy-user mailing list
>>> [hidden email]
>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>
>
>


_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev
Reply | Threaded
Open this post in threaded view
|

Re: [galaxy-dev] [galaxy-user] Custom java tool

Nils Homer
That should be sufficient.  Thanks,

Nils


On 5/27/10 1:13 PM, "Daniel Blankenberg" <[hidden email]> wrote:

> Hi Nils,
>
> At this point we're going to go with the approach that jars should be placed
> in the directory specified by '${GALAXY_DATA_INDEX_DIR}/shared/jars/',
> ordinarily this is 'GALAXY_ROOT/tool-data/shared/jars/', but the tool-data
> directory can be configured as the value of the 'tool_data_path' variable in
> universe_wsgi.ini.
>
>
> This allows jars to be accessible in tool configurations by specifying e.g.
> '${GALAXY_DATA_INDEX_DIR}/shared/jars/FOO.jar', where FOO.jar is the desired
> jar. Let us know if this is inadequate.
>
> (added in changeset: 3844:8fe924966a6a)
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On May 12, 2010, at 6:03 PM, Nils Homer wrote:
>
>> A jar bin would be great.  That would make it easy to add in new JARs.
>>
>>
>> On 5/12/10 1:22 PM, "Daniel Blankenberg" <[hidden email]> wrote:
>>
>>> Hi Nils,
>>>
>>> We do not currently have a best way to directly execute JARs in Galaxy. It
>>> does not appear that setting $classpath or $path, etc, will allow the direct
>>> execution of jars without providing the path or when not found in the
>>> current
>>> working directory.
>>>
>>> One simple possibility is for Galaxy to allow a configurable directory where
>>> required JARs can dropped / linked to; this variable would then be available
>>> for use in tool configurations.  Do you have any suggestions/ideas/thoughts?
>>>
>>>
>>> Thanks for using Galaxy,
>>>
>>> Dan
>>>
>>>
>>> On May 6, 2010, at 3:59 AM, Nils Homer wrote:
>>>
>>>> What is the best way to include wrap a JAR file in galaxy?  Also, what is
>>>> the best way to submit tools and their associated wrappers?
>>>>
>>>> Thank-you for your help in advance,
>>>>
>>>> Nils Homer
>>>>
>>>>
>>>> _______________________________________________
>>>> galaxy-user mailing list
>>>> [hidden email]
>>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>>
>>
>>
>


_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev